LOWER CLARK FORK RIVER FISHERY ASSESSMENT Project
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LOWER CLARK FORK RIVER FISHERY ASSESSMENT Project Completion Report Idaho Tributary Habitat Acquisition and Enhancement Program Prepared by: Robert Ryan Regional Fisheries Biologist Idaho Department of Fish and Game and Robert Jakubowski Natural Resources Technician Avista Corporation May, 2012 Lower Clark Fork River Fishery Assessment Lower Clark Fork River Fishery Assessment ................................................................................................ i ABSTRACT .................................................................................................................................................. ii INTRODUCTION ........................................................................................................................................ 1 STUDY AREA ............................................................................................................................................. 2 METHODS ................................................................................................................................................... 4 RESULTS ..................................................................................................................................................... 6 DISCUSSION ............................................................................................................................................. 13 RECOMMENDATIONS ............................................................................................................................ 15 ACKNOWLEDGEMENTS ........................................................................................................................ 15 LITERATURE CITED ............................................................................................................................... 16 i ABSTRACT A new minimum flow in the Clark Fork River below Cabinet Gorge Dam in Idaho was negotiated in 1999 as part of Avista Corporation’s relicensing agreement for Cabinet Gorge Dam. Minimum instream flow was increased from 84.9 cms to 141.5 cms. Increased minimum flows were hypothesized to increase the availability of rearing habitat for fish and improve foraging conditions by providing more stable habitat conditions for aquatic invertebrates. Subsequent effects of these changes were expected to include increased abundance of target fish, increased proportion of younger age classes of target species, and improved condition of all age classes. To describe the effects of increased minimum flows, fish populations were monitored between 1999 and 2008 in a 6.6 km reach of the lower Clark Fork River. Targeted species in the monitoring program included brown trout Salmo trutta, mountain whitefish Prosopium williamsoni, rainbow trout Oncorhynchus mykiss, and westslope cutthroat trout O. clarkii lewisi. Assessment focused on monitoring changes in abundance, size structure, and condition of fish populations in the affected area. Abundance of target species was estimated during annual monitoring efforts using mark recapture techniques. Relative abundance (catch per unit effort (CPUE)) of all species was estimated during fall sampling events. Size structure of sampled target species was compared by sample year using structural indices including proportional stock density and quality stock density. Physical condition of target species was evaluated by estimating mean relative weights. Estimated abundance of mountain whitefish ranged from 3,717 to 9,029 over the study period. Brown trout, rainbow trout (includes rainbow trout hybrids), and westslope cutthroat trout abundance estimates ranged from 76 to 356 fish per species, in the study area over the ten year period. No significant changes or trends in relative abundance were detected for any of the target species. Native non-game fishes including northern pikeminnow Ptychocheilus oregonensis, redside shiner Richardsonius balteatus, peamouth Mylocheilus caurinus, and largescale sucker Catostomus macrocheilus were the most common fishes sampled. Trends in structural indices were generally positive except brown trout quality stock density. Significant trends were only observed in mountain whitefish proportional stock densities and rainbow trout quality stock densities. Mean relative weights of westslope cutthroat trout, rainbow trout, and mountain whitefish were consistently above 80 while brown trout were consistently near or below 80. No significant linear relationships were observed between year and relative weight. Results suggested abundance, size structure, and condition of fish populations in the lower Clark Fork River were largely unchanged following increases in minimum flow below Cabinet Gorge Dam. ii INTRODUCTION An agreement reached with Idaho Department of Fish and Game (IDFG) in 1973 provided for a 3,000 cfs minimum flow below Cabinet Gorge Dam. That agreement was based on field assessments of the river at varying flows, electrical generating requirements, a review of historic low-flow records, and the earlier recommendation for a minimum flow of the same amount made by the U.S. Fish and Wildlife Service (Service). However, minimum flow in the Clark Fork River below Cabinet Gorge Dam was still one issue of concern to the local stakeholders involved in a collaborative relicensing process conducted by Avista Corporation (Avista; formerly Washington Water Power (WWP)) for Cabinet Gorge and Noxon Rapids dams. Avista relicensed these two hydroelectric facilities on the Clark Fork River in Idaho and Montana in 1999 and the Clark Fork Settlement Agreement (CFSA) was the product of the collaborative relicensing process (Avista 1999). Cabinet Gorge Dam is located just inside the Idaho border and Noxon Rapids Dam is located approximately 32 km upstream in Montana (Figure 1). A new minimum flow was negotiated for Cabinet Gorge Dam as part of the relicensing agreement, which increased the base flow from 84.9 cms (3,000 cfs) to 141.5 cms (5,000 cfs) (Avista 1999, see Appendix T). The objective of the increased minimum flow was to increase the amount of permanently wetted river habitat to benefit the aquatic resources of the Clark Fork River. More specifically, the objectives were to reduce the range of depth and velocity fluctuations in the river, and reduce varial zone and bar dewatering to increase stability of shoreline rearing areas for fish and enhance microinvertebrate production. Photo documentation was used to estimate the minimum flow needed to provide a meaningful increase in permanently wetted perimeter of the Clark Fork River (Beak 1997). Cabinet Gorge Dam is operated as a load following facility, with daily flow fluctuations ranging from 84.9 cms (3,000 cfs) to 1,010.3 cms (35,700 cfs) prior to the increased minimum discharge. Following the increase of minimum flow, generation capabilities were increased and daily flow fluctuations ranged from 141.5 cms (5,000 cfs) to 1076 cms (38,000 cfs). In addition to increasing minimum flows in the Clark Fork River, Avista and IDFG completed a restoration project in 2001 to provide perennial flow through the approximately 2 km-long Foster Bar side-channel to enhance fish habitat. This involved lowering several hydraulic control points within the side-channel so that water would flow through the side-channel over the range of discharges from Cabinet Gorge Dam. Prior to relicensing, when discharge from Cabinet Gorge Dam dropped below approximately 311.3 cms (11,000 cfs), the side-channel would become a series of un-connected pools. This reconnection was anticipated to provide valuable off-channel spawning and rearing habitat for salmonids, which is in limited supply in the Idaho reach of the Clark Fork River. To assess the effectiveness of changes in minimum flow and channel alteration, a ten-year monitoring program was conducted from 1999 through 2008. Increasing minimum flows from 84.9 cms to 141.5 cms was hypothesized to increase the availability of rearing habitat for fish and improve foraging conditions by providing more stable conditions for aquatic invertebrates. In addition, consistent flow and channel improvements in the Foster side-channel were expected to provide additional spawning and rearing habitat for salmonids. Subsequent impacts of these changes were hypothesized to increase abundance of target fish, increase the proportion of younger age classes of target species, and improve condition of all age classes. Assessment of 1 these two possible actions focused on monitoring changes in abundance, size structure, and condition of fish populations in the affected area. Limited quantitative information existed relative to the fishery resources of the Clark Fork River in Idaho prior to this study and prior to influences of hydropower facilities on the lower Clark Fork River. Several studies have investigated river use by adfluvial fish from Lake Pend Oreille (LPO), as well as the fish community composition (Heimer 1965, Anderson 1978, WWP 1995 and 1996). Avista, in preparation for their hydropower license renewal, conducted investigations into relative abundance of fish species present in the Clark Fork River in Idaho (WWP 1995 and 1996). The information contained in these Avista reports adds to our baseline knowledge of fish populations in the Clark Fork River. In combination, the earlier Avista work and the first several years of this investigation formed the baseline from which the effects of the increased minimum flow were judged. Required monitoring of the impacts of increased minimum flow below Cabinet